Repositories list

• octopus

  Public
  Bayesian haplotype-based mutation calling

  bioinformaticsgenomicssomatic-variants+ 6variant-callingsingle-cellphasingde-novo-mutationhaplotypesvariants

  C++

  •

  MIT License

  •37•305•48•0•Updated Aug 12, 2023Aug 12, 2023

• smcsmc

  Public
  Demographic inference from whole genomes

  C++

  •

  GNU General Public License v3.0

  •4•11•2•1•Updated Oct 18, 2022Oct 18, 2022

• polyploid

  Public
  Benchmarking variant calling in polyploids

  Jupyter Notebook

  •

  MIT License

  •2•13•0•0•Updated Nov 26, 2021Nov 26, 2021

• single-cell

  Public
  Benchmarking single-cell DNA variant calling

  Jupyter Notebook

  •

  MIT License

  •0•2•0•0•Updated Aug 10, 2021Aug 10, 2021

• luntergroup.github.io

  Public
  0•0•0•0•Updated Jun 9, 2021Jun 9, 2021

• octopus-paper

  Public
  Paper for octopus variant caller

  Jupyter Notebook

  •0•4•0•0•Updated May 7, 2020May 7, 2020

• analysis

  Public
  Analysis of inference methods on standard population models

  Python

  •

  MIT License

  •13•0•0•0•Updated Aug 1, 2019Aug 1, 2019

• stdpopsim

  Public
  A library of standard simulation models for msprime

  Python

  •

  MIT License

  •90•0•0•0•Updated Jul 31, 2019Jul 31, 2019

• EquivariantNetworks

  Public
  Python

  •0•4•0•0•Updated Sep 20, 2018Sep 20, 2018

• smcsmcScrm

  Public
  scrm jz_stable branch

  C++

  •

  GNU General Public License v3.0

  •7•0•0•0•Updated Jun 10, 2018Jun 10, 2018

• bamsplit

  Public
  Split a BAM file by haplotype support

  bam-filesbioinformaticshaplotypes+ 1variants

  Python

  •

  MIT License

  •1•16•1•0•Updated Dec 13, 2017Dec 13, 2017

• utilities

  Public
  Python

  •2•0•5•0•Updated Aug 4, 2016Aug 4, 2016